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xryanglab / RiboMiner

a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
https://pubmed.ncbi.nlm.nih.gov/32738892/
GNU General Public License v3.0
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PlotMetageneAnalysis for CDS and UTR for more than two groups #12

Closed nitishkumarmishra closed 9 months ago

nitishkumarmishra commented 1 year ago

Hi, I am using the below command to generate a metaplot for CDS regions- PlotMetageneAnalysis -i output_prefix/Riboseq_all_CDS_normed_dataframe.txt -o output_prefix/Riboseq_all_CDS_normed -g Ctrl,TGFb,CX5461 -r Ctrl-1,Ctrl-2,Ctrl-3TFGb-1,TGFb-2,TGFb-3CX5461-1,CX5461-2,CX5461-3 -U codon -u 0 -d 500 --mode mean --CI 0.95 --axhline 1

Once I use this command, I get all three PDF files for metagene analysis. Riboseq_all_CDS_normed_metagenePlot.pdf Riboseq_all_CDS_normed_mean_start codon.pdf Riboseq_all_CDS_normed_mean_stop codon.pdf

Surprisingly start/stop codon pdf plots have only two groups (CX5461 and Cntrl). Why I am not getting the third one in this plot? Is start/stop codon region metagene plots allow only two groups? I also realized Riboseq_all_CDS_normed_mean_dataframe.txt file has values for only Cntrl and CX5461, third one is missing.

--Nitish

nitishkumarmishra commented 1 year ago

It's my mistake. There was a typo error in one sample name.